should you disable the o2 sensor when dataloggin/tuning?
This depends on how you want to run your bike after tuning.
If you want it running with O2 disconnected, then disconnect O2 before tuning. Tune to whatever seems fit, but you should be aware that you need to adjust fuel to changes in altitude and air pressure manually (for XB models without MAP and baro sensors). This is most easily done by adjusting AFV, as the full map is OL now.
If you want to run it with O2 connected, then leave everything as is. But you have to tune the calibration mode area first, as calibration will impact AFV and therefore needs to be adjusted before touching OL regions. Use EGO correction as direction how to adjust map values, because this is what the ECM uses as feedback. (MLV users have to edit the equations in the VE analyzer for that.) When done correctly AFV will not change any more when walking through different parts of the calibration area. If AFV is moving without changes in altitude or air pressure, always check fuelling in calibration mode first, as this is the main reason.
Once the calibration mode area is done, proceed to the closed loop area. Then run the bike in calibration mode again, that a valid AFV is stored, as will be the case on the road later on. The last area tuned is OL and OL-WOT. AFV will not move any more and there's no need to freeze it by setting new limits in the ECM.
If it seems impossible to get a stable AFV, it's impact could be adjusted by changing the AFV's increase/decrease factors and number of transitions. The factors are set to approximately 5% and require 21 transitions in a stock setup. But in such cases a move to runnning the engine with O2 disconnected seems appropriate IMO.